Step 1

Place 8 ounces cream cheese in the bowl of a stand mixer (or large bowl if using an electric hand mixer). Let sit at room temperature until softened, about 30 minutes. Meanwhile, arrange a rack in the middle of the oven and heat to 350°F. Line a standard 12-well muffin pan with paper liners.

Step 2

Add 1 teaspoon of the vanilla extract to the cream cheese. Beat with the paddle attachment on medium speed until fluffy, about 1 minute. Scrape down the sides of the bowl and the beater with a rubber spatula. Add 1/3 cup of the granulated sugar, 1 of the large eggs, and 1/4 teaspoon kosher salt. Beat on low speed until combined and mostly smooth (a few lumps are okay), about 1 minute more. Add 1/2 cup mini chocolate chips and beat on low speed until just combined.

Step 3

Bring 1/2 cup water to a simmer in a small saucepan over medium heat. As soon as the water comes to a simmer, turn the heat off. (Alternatively, use an electric or stovetop tea kettle and bring it to a boil.)

Step 4

Place 3/4 cup all-purpose flour, the remaining 3/4 cup granulated sugar, 1/2 cup unsweetened cocoa powder, 3/4 teaspoon baking powder, 3/4 teaspoon baking soda, and the remaining 1/2 teaspoon kosher salt in a medium bowl. Whisk to combine.

Step 5

Add the remaining 1 large egg, 1/2 cup milk, 1/4 cup canola or vegetable oil, 2 teaspoons apple cider or white vinegar, and 1 teaspoon vanilla extract. Whisk to combine. Pour in the hot water and whisk to combine. The batter will be quite thin.

Step 6

Divide the batter evenly between the wells in the pan, filling each no more than 3/4 full. Dollop each with 2 tablespoons of the cream cheese mixture, dividing it evenly among the cupcakes.

Step 7

Bake until a toothpick inserted in the center of the cupcakes comes out clean, about 25 minutes. Let the cupcakes cool in the pan for about 10 minutes, then transfer to a wire rack to cool completely.